Tuesday, 30 July 2013

Global Species Database Spotlight: Gracillariidae

Jurate De Prins in the Congo

Global Species Database name:
Global Taxonomic Database of Gracillariidae (Lepidoptera)

Your name:
Jurate De Prins

Your position:
Taxonomic Editor and compiler of the Database

Where is the database located?
Belgian GBIF Mode – Belgian Biodiversity Platform

What taxa does your database cover?
A family of moths from the order Lepidoptera

How many species names do you hold? 
2351 species-group names

How many synonyms?

How and when did the database come about?
In 2005, we published the book World Catalogue of Insects. Volume 6. Gracillariidae. Apollo Books, 502 pp. ISBN 87-88757-64-1 and realized that no matter how robust and complete catalogues are, they are out of date on the day they are published. Only constantly updated information online can satisfy the needs. We realized very well that every species-group name with full taxonomic, biological and distribution information should be easily retrievable. This is the way how it should be and we should create a searchable and interactive relational database. Willy had the IT skills and knowledge so, we know how to do that. I also shortly worked as an executive officer at the European Network for Biodiversity Information in the programme ‘Making non-European biodiversity data in European repositories globally available’. It was my primary interest that every person all over the world, especially in Africa, interested in taxonomy can get correct, verified, structured and freely available taxonomic information. This was my sincere intention. Therefore, another taxonomic database, AfroMoths, covering all taxa of moths of the Afrotropical region and presenting 35,474 species-group names, is launched online as well www.afromoths.net.

How many people work on the database? 
Two persons (Jurate & Willy De Prins for data entry and taxonomic verification) and one person Nicolas Noé for launching the data online.
Neolithocolletis nsengai

What software do you use? 
Microsoft Access

How complete is it? 
It is 100% complete.

Is it continuing to grow and if so, how? 
Yes, almost daily I add distribution information. Also I myself and my colleagues describe new species in Gracillariidae, mostly from the tropical regions.

Are there any interesting areas of taxonomic contention within your group? 
It is phylogenetically a very interesting group of mining moths with the most intimate interrelation with a great variety of plants.

Do you have a favourite species or group of taxa (if yes please tell us why)?
My favourite subfamily is Lithocolletinae. I like these moths because they are so special; they are small, but very attractive and beautiful, have a global distribution and a very interesting biology. Their taxonomic history is so interesting as the best detective story. Furthermore, they are an outstanding object for a great variety of studies because many exceptions from generally accepted theories can be found in Lithocolletinae. They are really very special.

Do you have any fun or unusual names in your group (ie named after famous people)? 
Almost all species names in Gracillariidae have a special meaning and there are a lot of species within this family named after famous and not so famous but dedicated and nice people.

What made you choose a career in taxonomy? 
Because I like very much the Museum work: all aspects related to it from arranging the collection to writing papers, describing species, receiving interesting people, giving courses on collection management, organizing expeditions, collecting new and rare species in wild and remote places, giving presentations at international congresses. I truly think that this is the best job in the world.

Do you think traditional taxonomy has a future? 
Yes of course, but the methods will be very different and modern: 3D visualization of objects, virtual collections, virtual musea, creating huge global taxonomic and molecular reference libraries, linking those datasets etc. A very modern digital collection management and curation system will be certainly implemented. Taxonomy will become completely different from what it was before: it will stop being an occupation of slightly crazy people but will gain the vision of open science, open data and open community of international researchers working in a virtual research environment.

What is the most exciting recent taxonomic development in your group (if any)?
The breakthrough to the Afrotropical Region and making Africa the best taxonomically studied continent for Lithocolletinae. Please refer to the publication available at http://www.mapress.com/zootaxa/list/2012/3594.html

If you had the funds what improvements (if any) would you make to the database? 
I would like very much to implement images of species (we have started already), also interactive identification keys with images of internal structures, to link this database with the molecular reference library in BOLD and to show the up-to-date phylogenetic tree of Gracillariidae and related taxa taking the generic level as the basal monophyletic taxon based on highly reliable molecular and morphological evidences.

Do you submit to any other biodiversity aggregators than the CoL? 
Yes, this dataset is mirrored by the CoL and GBIF

Monday, 29 July 2013

Taxon of the Day: Kopsiopsis hookeri

Kopsiopsis hookeri 

When passing this plant you would be forgiven for thinking that a couple of pine cones had an amazingly fortuitous and synchronised landing. On further inspection you realise that perhaps that may not be the most accurate assessment and move on to a different thought - What is that?

Kopsiopsis hookeri (Walp.) Govaerts or Hooker's groundcone is a parasitic plant found in North West America (including Canada hence another common name Vancouver groundcone) that takes its food from another plant's (most noteably Gaultheria shallon) underground roots, rather than through photosynthesis or other means. They can grow a few inches in height and like their common namesake have overlapping scale-like leaves that are superficially similar to that of a conifer cone. The flowers range in colour from yellow to red to dark purple and bloom between June and July.

Kopsiopsis is a member of the almost completely parasitic plant family Orobanchaceae in the order Lamiales. Up until 1995 it was widely thought to be part of the genus Boschniakia, but taxonomic work carried out by Kew as part of a large ongoing world checklist initiative segregated this genus. This was later supported by DNA analysis. This circumscription was then adopted by ITIS Regional during their own taxonomic updates.

CoL Annual Checklist: Kopsiopsis hookeri
CoL contributor: ITIS Regional
Image copyright: R L F Matthias

Friday, 26 July 2013

Taxon of the Day: Asclepias speciosa

Asclepias speciosa - Showy milkweed

Asclepias speciosa Torr. or Showy milkweed is native to western North America and is part of a group of plants commonly and collectively known as milkweeds due to the milky sap in the stems and leaves. The etymology of the scientific name once again comes from Greek mythology with Linneaus naming the genus after the Greek god of healing Asclepius due to its many medicinal uses. The species epithet speciosa translates to beautiful or showy as in the common name, and never has a truer word been written, as this is a visually striking plant. Yet from a distance you may think nothing of it because in bud it can look quite nondescript, with greyish-green leaves and a hairy brownish head. But on closer inspection when in flower, you will find the most wondrously sculpted and intricately organised light-pink inflorescence.

Single flower
Each plant's head has numerous flowers forming what seems like a sphere, although in reality they are more like an umbrella, with all pedicels attached at the same place on the stem. Each individual flower has five petals bent backwards with five stamens fused into a tube, each with an horn-like appendage (see image above) attached. Because of its rhizomatous growth habit, you will often find it growing in large clumps, making it even more spectacular in the wild.

Once part of the Asclepiadaceae family since APGII  it is now treated as a sub-family of Apocynaceae. The Catalogue of Life follows APGIII groupings at family level but to create a unified and simplified checklist across all kingdoms the rank of subfamily is not used.

There is much more to know about this plant, its long history and variety of medicinal use as well as its close association with butterflies and other insects who rely on it, however today on Taxon of the Day we are superficially focusing on its good looks.

CoL Annual Checklist: Asclepias speciosa
CoL contributor: ITIS Regional
Image copyright: R L F Matthias

Thursday, 25 July 2013

Taxon of the Day: Erysiphales

Ascomycota - powdery mildew

Today’s Taxon of the Day looks at powdery mildew which includes the white moldy stuff that we often see seemingly dusted on plants. They are in fact a large group of related taxa within fungi, one of the seven kingdoms included in the Catalogue of Life. This entry has been produced by Oli Ellingham, he writes:

More than 95% of fungi are found within just two major phyla, the Ascomycota and Basidiomycota. The Erysiphales are an order of biotrophic fungi within the Ascomycota phylum, which are better and more commonly known as powdery mildews. They survive and thrive on green plants using chemical alterations within leaves, stems, flowers and fruits to shunt sugars manufactured by the plant towards its own branch-like hyphal protrusions. These appear as a powdery white, grey or black coatings on the surface of infected plants which cause a decrease in photosynthesis and a loss of nutrients to the fungi resulting in greatly reduced plant vigour. Once an extensive network of hyphae is established on a plant millions of spores are disseminated with the help of the wind and may fall on a new suitable host.

This is an order made up of more than 900 different species infecting almost 10,000 different species of trees, herbs and grasses. Individual species are identified using keys produced by experts which account for morphology of both asexual (anamorphic) and sexual (teleomorhpic) states of the fungus as well as its host species. However DNA base sequences are used in the lab and projects to identify individual powdery mildew species using molecular markers are on-going. Such molecular work has only provided taxonomic and phylogenetic debates with further fuel resulting in the names of tribes and genera being altered and positions of such genera and species being moved within the Catalogue of Life on numerous occasions.

One of the best known and most researched species of powdery mildew is Blumeria graminis (DC.) Speer 1975. This is a species so specialised to grass hosts that subspecies have formed to infect solely wheat, barley and other cereal crops. As such losses in yield of these crops have risen as high as 40% in North America. While fungicides have proved useful, resistant cultivars are also being developed to combat powdery mildew on a commercial scale. However pruning back extra growth of susceptible species, such as fruit trees and roses, to allow for significant aeration of individual leaves may help to prevent similar fungal outbreaks in your own garden.

CoL Annual Checklist: Erysiphales
CoL contributor: Species Fungorum
Image copyright: Maccheek

Tuesday, 23 July 2013

Filling gaps in the Catalogue of Life

Cyathea medullaris - a missing taxon

Global Species Databases (GSD) have been sending their taxonomic checklists to the Catalogue of Life (CoL) since 2000. On receipt of these checklists the CoL team integrates them into one unified checklist - The Catalogue of Life. This is both a routine procedure (as updates are periodically provided from the same GSDs) and a manual one because any new taxonomic data is subject to integrity checks by editors. This maintains the authoritative status of the CoL above all other global species checklists. However, maintaining an expert database has meant a cautious approach to adding species, and so to-date this checklist of the world's organisms is only 70% complete. It is disappointing to our users when they cannot find their taxon when in a gap area. Often it may be a well known organism (like the Black tree fern Cyathea medullaris shown above) making people wonder why it couldn't just add it. Well the answer is the Catalogue of Life does not add or annotate species itself, it only lists names adopted by expert taxonomists in their GSDs. If a name is not in one of the contributing GSDs or one of our proto-GSDs it will not be in the Catalogue of Life. 

So where are the other ~30% of known species names? Well one answer is that they may not be in an electronic global checklist format anywhere as yet. They may be in scientific publications or monographs, regional floras or faunas but not in a database. Alternatively, ones that do exist, may not have been submitted to the Catalogue of Life because the taxonomist in question is reluctant to hand over their hard earned data for public use. A checklist is the culmination of a great deal of taxonomic work and time. For some taxonomists who collected original data, it is their whole life's work. So to give it away for free is a big decision. When data is aggregated (as it is within the Catalogue of Life) there are all sorts of issues with attribution and individual property rights which makes for complexity in the supply and use of that data. This is why the Catalogue of Life explicitly links all data back to the GSD that supplied it, to give that GSD the maximum amount of credit and publicity for their work. And where that data is passed on to global biodiversity partners (Encylopedia of Life, GBIF, ENA, IUCN), the Catalogue of Life asks for continued attribution to the GSD in the partners' data portal. Luckily, this is enough for many GSDs and they are able to make that data readily available to the wider world, but perhaps if they were not so globally minded the Catalogue of Life would not exist. This is why the Catalogue of Life wants to promote taxonomists and the work they do, to ensure that it is not taken for granted by the end user.

To continue to fill gaps the Catalogue of Life team carries out the following activities: 1) it searches for taxonomists who have checklists and are willing to contribute; 2) it creates proto-GSDs where a possibility exists to do so; and 3) through the i4Life project, it funds taxonomists to create new GSDs to fill priority gap areas that it knows are of importance to global biodiversity partners (and hence end users). This last way is known as the 'Pilot Projects', a currently ongoing workflow within the i4Life project that aims to place as many new names and taxa from global biodiversity partners into scrutinised taxonomic checklists as possible and then supply them to the Catalogue of Life. The Catalogue of Life then, in turn, supplies them back to the global biodiversity partners, improving the quality of their taxonomic data in the process. The goal is both to add many thousands of new names to the Catalogue of Life (moving closer to the estimated 1.9m known species that are believed to exist somewhere in the world) and to create consistency in the quality of taxonomy partner databases.

Later on in the Catalogue of Life blog, we will look at the Pilot projects in greater detail. In the meantime if you type a species name into the search box and find that it is not there, please be reassured that the Catalogue of Life is fully aware of it, and is doing all it can to find a supplier for this taxon group. And if you are a student of taxonomy doing the typing, you may want to think about one day creating an electronic global species checklist and contributing to the Catalogue of Life community!

Image copyright: Public Domain

Monday, 22 July 2013

The World Congress of Malacology, Ponta Delgada, Azores, Portugal, 21-27/07/2013

Thomas Kunze presented a poster on behalf of the i4Life consortium at The World Congress of Malacology, Ponta Delgada, Azores, Portugal, 21-27/07/2013

Taxon of the Day: Yucca brevifolia

Yucca brevifolia - Joshua Tree
Back to the desert and to such a recognisable and iconic plant, Taxon of the Day is wondering if it is possible to say anything enlightening about it. Perhaps it is almost enough to show one, to remind everyone both what the Catalogue of Life is all about and what a beautiful and striking plant it is. Especially when viewed in its stark, native landscape, it creates mad shapes and vistas that are both surreal and unique in equal measure.

Endemic to the Mojave Desert (that crosses California, Utah, Arizona and Nevada) but perhaps with its greatest density in the self-titled Joshua Tree National Park, Yucca brevifolia Engelm. has many attributes of a tree - a trunk with branches, leaves, flowers and fruit. And it is these unquestionable similarities that have informed a number of its common names including the widely used Joshua Tree. However, it does not fit into either a coniferous or deciduous variety and is classified as a monocot in the plant family Asparagaceae.  As such it does not have growth rings,  thus making it difficult to estimate the age of one. Yet it is known that they can survive hundreds of years, if not thousands. Its branches can be extremely variable in habit, but generally go up and out, which is how it came to acquire the first part of its common name, where Mormon settlers who named it, thought it resembled Joshua from the bible, raising his arms up in supplication. Local indigenous peoples have their own names of course and have made use of the plant for food and materials for centuries.

Joshua Tree National Park
Yucca brevifolia is an indicator species for this desert region and as such it has had a relative amount of attention in terms of the potential impact of climate change, with declining numbers already recorded in hotter areas. Documenting biodiversity, including completing a list of all known species names is a priority if we hope to have the best tools to deal with these changes.

Whether global warming is a factor, or other environmental influences, perhaps the most interesting recent event for this plant was that 2013 has gone on record as one of the greatest years for flowering, with blooming Joshua Trees in great abundance over most of its range. What a wonderful sight to have seen first-hand.

CoL Annual Checklist: Yucca brevifolia
CoL contributor: World Checklist of Selected Plant Families
Image copyright: R L F Matthias

Friday, 19 July 2013

Taxon of the Day: Hyracoidea

Procavia capensis
The hyrax is a small to medium sized mammal with a rounded body, short stubby legs, small tail and cute face.  There are a total of four living species that make up the entire order Hyracoidea, all with superficially similar looks. They have a wide geographical and altitudinal range in Africa and parts of the Middle East, where they occupy a number of different habitats as depicted in their common names (see below), but are famous for liking a rocky outcrop to sunbath on that has easy access to hiding places from predators when tanning. However, similar to another recent Taxon of the Day Procyon, they are finding these requirements elsewhere, most notably in urban areas causing them to achieve pest status in some places. To enable them to scramble up rocks at fast pace they have special padded feet that sweat giving them added grip. Interestingly, they are a member of the Afrotheria group, which makes them closely related to elephants, a relationship that has been supported by fossil, morphological and more recently molecular analysis.

The order Hyracoidea contains one family Procaviidae with three genera. The four remaining species are Dendrohyrax arboreus (Southern tree hyrax), Dendrohyrax dorsalis (the Western tree hyrax) Heterohyrax brucei (Yellow-spotted rock hyrax) and Procavia capensis or (Rock Hyrax) shown in the picture above. There are, not surprisingly considering its distribution, many more common and regional names than those given above,  for example in South Africa the hyrax is affectionately known as a Dassie.

Also of note is their sophisticated and romantic communication patterns, where the male sings quite complex songs to the female when trying to sell themselves.  There are many videos of hyraxes on youtube and Taxon of the Day shares its favourite below.

CoL Annual Checklist: Hyracoidea 
CoL contributor: ITIS Global
Image copyright: R L F Matthias

Tuesday, 16 July 2013

Taxon of the Day: Viruses

Ebola virus

It may be surprising to some that viruses are included in the Catalogue of Life as they are often not thought to be alive until they infect their host. It is also not common to think of a virus as a species in the same way we do other organisms. However, what alive means is a debatable, philosophical human construct and is luckily outside the scope of Taxon of the Day today. In the second edition of the Catalogue of Life in 2002, it was agreed that viruses were part of life on earth.

What we do know is simply a virus is a small particle that can infect the cells of animals (including humans), plants, bacteria and other viruses. Their genome is made up of RNA or DNA in different formations and they often have a protein shell called the capsid. On its own a virus cannot multiply, but with the help of living cells it is given the energy to replicate. There are currently nearly 2,500 named viruses in the Catalogue of Life and allegedly millions more yet to be described. Viruses are classified primarily by their host organism, particle morphology and its genome type (eg DNA or RNA). There are additional identifiers too but these are the top three.

You can browse virus taxonomy in CoL
You can browse virus taxonomy in CoL
Now on to the taxonomy. One of the best features of the Catalogue of Life is the search and browse interface. You can find a name for an organism in a number of different ways depending on the information you start off with. You can also browse different parts of the taxonomic hierarchy comparing groups from kingdom down to species. There is no interface, with so many options to access data like it on the web and because of this, it is a quick and easy way to check a virus name, classification, browse different groups and print off species lists within the virus hierarchy. 

Like other kingdoms in the Catalogue of Life virus taxonomy is particular to its own taxa including its own set of nomenclatural rules. The Global Species Database of viruses is supplied by the the International Committee on Taxonomy of Viruses (ICTV) which since its inception in 1962 has become the singular authoritative source on virus taxonomy. It is run by a group of expert virologists where any new viruses that are named or need to be classified must be approved by the ICTV Executive Committee. Unlike some of the other taxon groups in the Catalogue of Life, it all seems rather uncomplicated. A 'universal taxonomy of viruses' it doesn't get much clearer than that.

In practice it is similar to other biological classification systems, as the ICTV recognises the ranks of order, family, subfamily, genus, and species. It does not recognise ranks above order and it does not concern itself with taxa below species. So whilst strains, variants, types etc are the interests of many a virologists and where known are assigned to species, in the classification system they do not have a recognised rank.

For simplicity and unification between other kingdoms the Catalogue of Life supports all used ranks of the ICTV with the exception of subfamily. In addition, because the Catalogue of Life supports the binomial naming of species - where genus and species epithet make up a name it is different to virus taxonomy, where the species name is just the species epithet name (in the Catalogue of Life). For the user of the Catalogue of Life this is not so important as all the essential information is there just displayed slightly differently than you may find it in the ICTV database.

For example the taxonomy of two well know viruses found in the Catalogue of Life.

Ebola is classified as:
- Order Mononegavirales
   - Family Filoviridae
      - Genus Ebolavirus
         - Species epithet zaire ebolavirus ICTV

Where species name in CoL is written as Ebolavirus: zaire ebolavirus ICTV where the colon is an indicator of the differing taxonomies.

HIV is classified as:
- Order Unassigned
   - Family Retroviridae
    - Genus Lentivirus
      - Species epithet: human immunodeficiency virus 1 ICTV

Where species name is Lentivirus: human immunodeficiency virus 1 ICTV

However to a virologist or probably anyone else, you would say 'human immunodeficiency virus 1 is a species of the genus Lentivirus of the family Retroviridae'.

CoL Annual Checklist: Viruses
CoL contributor: ICTV
Image copyright: Public Domain

Monday, 15 July 2013

Taxon of the Day: Liriodendron

Liriodendron tulipifera - Tulip tree
The distinctive shape of the leaves (a botanist may call it truncate-retuse!) of Liriodendron tulipifera L. is quite unlike any other tree, and the tulip-shaped green and orange flowers in spring give the tree one of its common names - the Tulip tree. It is also one of the tallest (can reach over 50m) and straightest of deciduous trees, which in the right conditions can have a rapid growth rate when young. Consequently, it has a history of being an economically important timber product as well as aesthetically, extremely pleasing. If that were not enough, its pendulous leaves flutter and rustle in the slightest breeze (perhaps giving rise to another of its common names the Yellow poplar) making it, not surprisingly, a popular ornamental for centuries.

Liriodendron leaves
In the Catalogue of Life Liriodendron is one of two genera (the other being Magnolia) in the primitive plant family Magnoliaceae. In terms of species Liriodendron is a tale of two halves: the aforementioned Liriodendron tulipifera is native to eastern USA, common, hardy, and widely planted in temperate climes; whereas Liriodendron chinense (Hemsl.) Sarg. is native to central and southern China and northern Vietnam, less hardy, and in its native habitat (montane evergreen broadleaved forest) is listed as near threatened by the IUCN Red List. There have been concerted efforts to preserve this primitive species in introduced habitats, for example a Tulip tree avenue composed of Liriodendron chinense can be seen in Kew Gardens since 2001. In the wild there are some protected areas yet how successful these measures have been needs reassessing.

The disjunct geographical distribution of Liriodendron (ie opposite sides of the globe) is due to major geologic events causing separation in its ancient past. Where the isolation that occured led to each species evolving slightly different characteristics. Recent genetic research reports that the Tulip tree is the least evolved of any flowering plant currently assessed, having retained ancestral traits lost by other plants in its millions of years of evolution. As a result, this wonderful plant could end up helping explain the evolution pattern of all flowering plants.

CoL Annual Checklist: Liriodendron 
CoL contributor: World Checklist of Selected Plant Families
Image copyright: R L F Matthias

Thursday, 11 July 2013

Taxon of the Day: Prunus dulcis

Prunus dulcis - Almond Tree

Today’s Taxon of the Day has been produced by Maria Christodoulou she writes:

Described as crazy by locals in the Mediterranean the almond tree,
Prunus dulcis (Mill.) D.A.Webb, is certainly one of the eccentrics in the region. Its early flowering times, sometimes as early as February, have made it a symbol of hope and regeneration. Being a flowering time pioneer however has its costs, with the first flowers often destroyed by frost. 

Considered one of the first nuts to be domesticated, the almond tree has a most definite dark side. The seed in its wild state produces sufficient levels of amygdalin which are transformed into cyanide when eaten. The domestication selection process, aided by the fact that it is relatively easy to grow from seed, is dated back to the Bronze Age. A low level presence of amygdalin still remains today, but it is mostly found in bitter almonds grown almost exclusively for medicinal reasons. 

The uniqueness of the almond always captured the imagination of the locals with various customs and superstitions focusing on almonds – such as presenting newlyweds with sugar coated almonds. It is unsurprising therefore that the ancient Greeks had one of the most tragic love stories created to explain the flowering of the tree, the story of Phyllis and Demophon. According to legend Phyllis, who spent years waiting for her fiancé to return from Athens, died of sorrow without seeing him again. The gods, to honour her, planted a tree that never flowered. After many years, Demophon returned and searched for her only to find a dead tree. Overwhelmed by grief he embraced the tree and suddenly, in the middle of February, it flowered.

CoL Annual Checklist: Prunus dulcis
CoL contributor: IOPI Global Plant Checklist
Image copyright: Nicolás Pérez

Wednesday, 10 July 2013

Taxon of the Day: Cardiocrinum giganteum

Cardiocrinum giganteum

Taxon of the Day looks at one of the largest members of the Liliaceae family. Cardiocrinum giganteum (Wall.) Makino or Giant Himalayan Lily is native to the Himalayas and one of three species in the Genus Cardiocrinum all found in the Catalogue of Life. It has two known varieties Cardiocrinum giganteum var. giganteum found in the Himalayan regions of Bhutan, Myanmar, India and Nepal, and Cardiocrinum giganteum var. yunnanense native to southeast China. The other two species are distributed in eastern China (C.cathayanum) and Japan (C.cordatum) respectively. 

Cardiocrinum giganteum is a bulbous perennial growing to over 2m in height, with heart-shaped leaves and trumpet-shaped, white flowers with purple markings inside.

Giant Himalayan Lily
Cardiocrinum giganteum has been widely introduced as an ornamental garden plant in temperate areas, becoming naturalised and potentially invasive in certain areas of western New Zealand who have noted it as a 'weed of invasion stage-2' (Phartyal et al, 2012). Invasive species have a major impact on the environment, threatening biodiversity and reducing overall species abundance. Whilst the Catalogue of Life covers some 70% of the world’s known species, and is growing steadily in quality and coverage, we are still without a complete, comprehensive and global list of the Earth’s living species against which to measure biodiversity change.  

CoL Annual Checklist: Cardiocrinum giganteum
CoL contributor: World Checklist of Selected Plant Families
Image copyright: R L F Matthias

Tuesday, 9 July 2013

Taxon of the Day: Felis sylvestris grampia

Felis sylvestris grampia

To honour a very special week for one Scottish top cat, Taxon of the Day pays tribute to the Scottish Wildcat. Felis sylvestris grampia Miller, 1907 is a small cat (although 50% larger than the average domesticated cat) found now only in North East Scotland. There have been desperate calls in recent years to protect it from imminent extinction. Where once more widespread, hybridisation with domesticated cats has been cited as one of the reasons for its decline, with numbers thought to be as low as 35. However, recent DNA research on hybridisation is throwing new light on the situation and helping to design the most appropriate course of conservation action. Correct identification (using a pure wildcat genetic model for comparison) enables trapping followed by relocation to protected areas.

In modern biodiversity research there is a growing need to incorporate DNA data. Therefore the correct species identification of a specimen and precise labelling of DNA samples/sequences is essential. Through the i4Life project the Catalogue of Life cooperates with one of the biggest DNA databases worldwide - ENA at EMBL-EBI to enable easier and more accurate taxon based searches through their sequence database.

In the Catalogue of Life Felis sylvestris is one of seven species in the genus Felis which also includes Felis catus the domesticated cat. It is thought that the cat was domesticated from the African Wildcat about 10,000 years ago. 

Much more information on this species is available on the Scottish Wildcat Association website.

CoL Annual Checklist: Felis silvestris grampia
CoL contributor: ITIS Global
Image copyright: Peter Trimming

Monday, 8 July 2013

Taxon of the Day: Calypso bulbosa

Calypso bulbosa

On Taxon of the Day and in compiling the Catalogue of Life we appreciate a monotypic taxon because it allows us to move on to something else tomorrow having some sense of completion. We also enjoy a good name whether it be scientific or common. Calypso bulbosa (L.) Oakes or Venus's slipper fits the bill on both accounts, seductive name, taxonomically unique.

The only species in the genus Calypso in the family Orchidaceae, this plant is a perennial that grows from a round, bulb-like corm (hence bulbosa) 10-20 cm tall with a fragrant, white to pink to purple, solitary flower head. The lip of the orchid is pouch-like (hence slipper) and each plant has a single basal, oval leaf.  The distribution is circumpolar so you can find it typically in the northern coniferous forested regions of Northern Europe, Russia, Japan, US and Canada. Due to having a mycorrhizal dependence on fungi it is almost impossible to transplant or grow outside of its natural environment.

The etymology comes from Greek mythology where Calypso was a sea nymph in Homer's Odyssey, noted for her beauty and secretive behavior which is perfectly descriptive as it is known to favour the forest understory or similarly sheltered place. Thus finding one can prove quite difficult but when it happens it's memorable. For example in 1864 on meeting the Calypso after a long day of botanising the naturalist John Muir remarked - "It seemed the most spiritual of all the flower people I had ever met. I sat down beside it and fairly cried for joy." A full description of Muir's meeting with Calypso bulbosa (then known as Calypso borealis) can be found here

The Catalogue of Life lists four varieties of Calypso bulbosa all differing slightly in their appearance and distribution.

CoL Annual Checklist: Calypso bulbosa
CoL contributor: World Checklist of Selected Plant Families
Image copyright: R L F Matthias

Thursday, 4 July 2013

Taxon of the Day: Ceyx pictus

Ceyx pictus

Small is beautiful was never more true than for today's Taxon of the Day. Measuring around 12cm in length and weighing about 12g the African Pygmy Kingfisher or Ceyx pictus (Boddaert, 1783) is perfectly formed. One of seven species in the genus Ceyx this bird has a large range across sub-saharan Africa. This specimen was spotted in the Hluhluwe–Umfolozi Game Reserve in South Africa.

Taxonomy and phylogeny in the Kingfisher world has been rather turbulent over the years with difference of opinion over classification and species concepts. Catalogue of Life has all Kingfishers in the family Alcedinidae with 17 genera and 91 species in total. At genus level revisions based on molecular analysis have suggested that Ceyx in addition to Alcedo (which includes the Common Kingfisher A. atthis) as currently delimited may not be natural groups. Many taxonomic sources classify this species under the genus Ispidina, but in the ITIS database the two known species of this named genus have been absorbed under Ceyx with Ispidina pictus a synonym.

The etymology of Ceyx is from Greek mythology and pictus from Latin meaning painted which seems so appropriate as it looks as if it has been daubed by hand with a vibrant palette.  However, the species prefers to feed on mainly insects rather than fish making the later part of its common name seem rather redundant.

To listen to call sounds of Ceyx species (unfortunately not our featured one) go to the fantastic website xeno-canto supported by the Catalogue of Life's future funders Naturalis

CoL Annual Checklist: Ceyx pictus
CoL contributor: ITIS Global
Image copyright: R L F Matthias

Wednesday, 3 July 2013

What is a proto-GSD?

Gentianella amarella

We use the term Global Species Database when describing how the Catalogue of Life is put together. Global Species Databases or GSDs are ideally monographic databases with global coverage of all known species in one taxon. They can be integrated side-by-side with other GSDs without any overlap. In an ideal world the Catalogue of Life would assemble GSD after GSD to the point where all known species are covered. Unfortunately this ideal scenario does not exist and the Catalogue of Life has had to find different ways to increase coverage where gaps remain.

Tuesday, 2 July 2013

Taxon of the Day: Procyon

Procyon lotor - A pest? Me?

There are three species of Raccoon in the Catalogue of Life (CoL). The most common one, Procyon lotor  (Linnaeus, 1758), peering out of the photo,  is often regarded as a pest due to its infiltration of urban areas and other unexpected habitats. This particular one was found inhabiting a Thuja shrub in a back garden in downtown Vancouver. Its range is large, distributed throughout North America in addition to some countries in Europe and Asia as a result of its introduction in the mid-20th century.

However, they are not all so common as one of the three species - Procyon pygmaeus Merriam, 1901 is listed in the IUCN Redlist as Critically Endangered. The Cozumel Raccoon, as the name suggests, is only found on the paradisaical island of Cozumel off the East coast of Mexico. Although significantly smaller than the common one (it is often referred to as the Pygmy Raccoon hence pygmaeus) and with a slightly different shaped snout, its overall appearance is similar.  Its already small population is declining, with mature individuals thought to be less that 250, which along with its limited geographic range make it the subject of conservation action. Threats to the species have been identified as the impact of natural disasters particularly hurricanes, increasing tourism and alien invasive species such as the Boa constrictor.  The IUCN redlist is the world's most comprehensive inventory of the global conservation status of biological species. It is also a global partner in the i4Life project which is currently responsible for developing the Catalogue of Life. The IUCN Redlist links to the CoL using the CoL webservice allowing their users to get information on a species name they have searched for that is not in IUCN but is in CoL.  The fundamental  importance of that is that the user is reassured they have searched for a real species with a recognised spelling and is not tempted to try other spellings or to just give up their search. 

The final species of the three supplied by the ITIS Global checklist is the Crab-eating Raccoon or Procyon cancrivorus (G.[Baron] Cuvier, 1798) found in Central and South America.

CoL Annual Checklist: Procyon
CoL contributor: ITIS Global
Image copyright: R L F Matthias

Monday, 1 July 2013

Taxon of the Day: Cynara cardunculus

Cynara cardunculus
Today's Taxon of the Day Cynara cardunculus L. is both visually and orally pleasing. It was described by the herbalist John Gerard in 1633 in his book Herball or General Historie of Plantes as 'being pleasant to the taste, and good to procure bodily lust'. Much later in 2005 scientists showed it to be a natural serotonin reuptake inhibitor, causing a mood elevating effect. Its stately, architectural growth form in addition to its all round pleasure potential adds up to a very interesting plant.

From the Asteraceae family (in the thistle group) the Catalogue of Life lists two subspecies of Cynara cardunculus:  Cynara cardunculus subsp. flavescens found predominantly in the western Mediterranean and Cynara cardunculus subsp. cardunculus, found in the east, with both subspecies reportedly overlapping in Sicily. Morphologically the main difference between the two comes down to the shape and colouring of the bracts (the leaf like projections shown in the picture). 

The wild variety of the species is often referred to by the common name Cardoon, and the cultivated varieties that we buy in the supermarket as globe artichokes. The vegetable that we eat is the immature flower head which includes the bracts, the base known as the heart, and the middle area made of a mass of immature florets called the beard or the choke, which if left to grow would bloom into the purple flower head seen in the picture. The beard is generally discarded apart from in baby artichokes where the whole thing is eaten. 

It has been suggested that to test the freshness of an artichoke one should rub two together, if they squeak they are fresh if there is no sound, they are not.

CoL Annual Checklist: Cynara cardunculus
CoL contributor: Global Compositae Checklist 
Image copyright: R L F Matthias